<tool id="igvscreenshot" name="Take an IGV screenshot" version="1.2">

	<description>specifying tracks and a genomic location</description> 

        <requirements>		
		<requirement type="package" version="2.3.57">igv</requirement>
	</requirements>
        
	
	<command interpreter="bash">
		igvscreenshot.sh 
                    --build $reference
                    #for $i, $t in enumerate( $tracks )
                        --track ${t.inputfile}
                        --ftype ${t.inputfile.extension}
                        --view ${t.view}
                        --viewaspairs ${t.viewaspairs}
                        #if not $t.trackname  <!-- validator for empty field does not seem to work within a repeat, so this is the workaround  -->
                            #set $tracklabel = "noname"
                        #else
                            #set $tracklabel = $t.trackname
                        #end if
                        --label $tracklabel
                        #if $t.inputfile.extension == "bam"
                            --index $t.inputfile.metadata.bam_index
                        #else
                            --index "none"
                        #end if
                    #end for
                    --region "$region"       
	</command>


	<inputs>
	<!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions -->
                
                <param name="reference" type="select" label="Select Build">
                    <option value="hg18"> hg18 </option>
                    <option value="hg19"> hg19 </option>
		</param>
                
		<!-- file from history -->
                <repeat name="tracks" title="Track" min="1">
                    <param name="inputfile" type="data" format="bam,vcf,bed,gtf,gff" label="Select input file" help="choose input file from history"/>
                    <param name="trackname" type="text" size="100" value="track label" label="Track Label" >
                        <sanitizer>
				<valid initial="default"> 
					<add preset="string.printable"/> 
					<remove value=" "/>
				</valid> 
				<mapping initial="none"> 
					<add source=" " target="_"/>
				</mapping> 
			</sanitizer>                        
                    </param>
                    <param name="view" type="select" label="View settings of track" >
                           <option value="collapse"  > collapsed </option>
                           <option value="expand"  > expanded </option>
                           <option value="squish"  > squished </option>
                    </param>                    
                    <param name="viewaspairs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="view as pairs?" help="optional setting for paired-end data"/>
				
                </repeat>
                <!-- text field parameter -->
		<param name="region" type="text" size="100" value="chr:start-end" label="Enter region to visualise in IGV, format chr:start-end" help="to show multiple regions in a single image, use comma-separated list of regions, e.g. chr1:0-100,chr2:100-200"/>
    
                </inputs>

	
	<outputs>
		<data format="png" name="outputfile" from_work_dir="screenshot.png" label="IGV screenshot of region ${region} on ${on_string}"/>
	</outputs>

	<help>
This tool will create an IGV screenshot of the desired location(s) with the desired tracks.
        
Tracks may be bam, vcf, bed, gff or gtf format.

Multiple regions may be specified (comma-separated)


        
        </help>
</tool>